9-111362043-T-G

Variant names:

• chr9-111362043-T-G
• rs2098113894
• NM_001364929.1:c.5507A>C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001364929.1(ECPAS):​c.5507A>C​(p.Glu1836Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ECPAS NM_001364929.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.51

Genes affected

ECPAS (HGNC:29020): (Ecm29 proteasome adaptor and scaffold) Enables proteasome binding activity. Involved in ubiquitin-dependent ERAD pathway. Located in several cellular components, including centrosome; cytoplasmic vesicle; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.17525169).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ECPAS	NM_001364929.1	c.5507A>C	p.Glu1836Ala	missense_variant	Exon 50 of 50	ENST00000684092.1	NP_001351858.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ECPAS	ENST00000684092.1	c.5507A>C	p.Glu1836Ala	missense_variant	Exon 50 of 50		NM_001364929.1	ENSP00000507419.1
ECPAS	ENST00000259335.8	c.6041A>C	p.Glu2014Ala	missense_variant	Exon 51 of 51	1		ENSP00000259335.4
ECPAS	ENST00000338205.9	c.5507A>C	p.Glu1836Ala	missense_variant	Exon 49 of 49	5		ENSP00000339889.5
ECPAS	ENST00000374383.1	c.416A>C	p.Glu139Ala	missense_variant	Exon 4 of 4	2		ENSP00000363504.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Alfa AF: 0.0000312 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.051	T
BayesDel_noAF	Benign	-0.31
CADD	Benign	22
DANN	Uncertain	0.99
DEOGEN2	Benign	0.059	.;.;T
Eigen	Benign	0.16
Eigen_PC	Uncertain	0.30
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Uncertain	0.90	.;D;T
M_CAP	Benign	0.016	T
MetaRNN	Benign	0.18	T;T;T
MetaSVM	Benign	-0.84	T
PrimateAI	Uncertain	0.59	T
PROVEAN	Benign	-1.7	N;N;.
REVEL	Benign	0.17
Sift	Benign	0.051	T;D;.
Sift4G	Benign	0.16	T;T;D
Vest4		0.30
MutPred		0.10		.;Gain of MoRF binding (P = 0.0302);.;
MVP		0.13
MPC		0.26
ClinPred		0.74	D
GERP RS		5.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
gMVP		0.15

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2098113894; hg19: chr9-114124323; COSMIC: COSV52203284; COSMIC: COSV52203284;